WO2019050898A1 - Procédés et compositions pour traiter une maladie cutanée inflammatoire - Google Patents

Procédés et compositions pour traiter une maladie cutanée inflammatoire Download PDF

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Publication number
WO2019050898A1
WO2019050898A1 PCT/US2018/049477 US2018049477W WO2019050898A1 WO 2019050898 A1 WO2019050898 A1 WO 2019050898A1 US 2018049477 W US2018049477 W US 2018049477W WO 2019050898 A1 WO2019050898 A1 WO 2019050898A1
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Prior art keywords
coding sequence
recombinant microorganism
seq
filaggrin
polypeptide
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PCT/US2018/049477
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English (en)
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Travis Michael WHITFILL
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Azitra Inc
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Priority to EP18854435.7A priority Critical patent/EP3678640A4/fr
Priority to AU2018328119A priority patent/AU2018328119A1/en
Priority to CA3074823A priority patent/CA3074823A1/fr
Priority to KR1020207009609A priority patent/KR20200051001A/ko
Priority to CN201880071303.9A priority patent/CN111278447A/zh
Priority to JP2020513607A priority patent/JP2020536499A/ja
Publication of WO2019050898A1 publication Critical patent/WO2019050898A1/fr
Priority to JP2023160723A priority patent/JP2024009822A/ja

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/66—Microorganisms or materials therefrom
    • A61K35/74—Bacteria
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/74—Vectors or expression systems specially adapted for prokaryotic hosts other than E. coli, e.g. Lactobacillus, Micromonospora
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K9/00—Medicinal preparations characterised by special physical form
    • A61K9/0012—Galenical forms characterised by the site of application
    • A61K9/0014—Skin, i.e. galenical aspects of topical compositions
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • A61K38/17—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • A61K38/1703—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • A61K38/1709—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • A61K38/17—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • A61K38/177—Receptors; Cell surface antigens; Cell surface determinants
    • A61K38/179—Receptors; Cell surface antigens; Cell surface determinants for growth factors; for growth regulators
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/02—Bacterial antigens
    • A61K39/085—Staphylococcus
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P17/00—Drugs for dermatological disorders
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4713—Autoimmune diseases, e.g. Insulin-dependent diabetes mellitus, multiple sclerosis, rheumathoid arthritis, systemic lupus erythematosus; Autoantigens
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/71—Receptors; Cell surface antigens; Cell surface determinants for growth factors; for growth regulators
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N1/00—Microorganisms, e.g. protozoa; Compositions thereof; Processes of propagating, maintaining or preserving microorganisms or compositions thereof; Processes of preparing or isolating a composition containing a microorganism; Culture media therefor
    • C12N1/20—Bacteria; Culture media therefor
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
    • C07K2319/02—Fusion polypeptide containing a localisation/targetting motif containing a signal sequence
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
    • C07K2319/10—Fusion polypeptide containing a localisation/targetting motif containing a tag for extracellular membrane crossing, e.g. TAT or VP22

Definitions

  • Atopic dermatitis is a chronic, pruritic, inflammatory skin disease that affects 5-20% of children worldwide (Williams, H., et al. J Allergy Clin. Immunol.
  • atopic dermatitis patients had markedly higher prevalence of allergies (46% vs. 20%), asthma (22% vs. 8%), anxiety (43% vs. 21%), and depression (37% vs. 21%)
  • dysbiosis or a microbial imbalance, the severity of which is associated with disease severity; see Kong, H. H., et al. Genome research. 2012;22(5):850-859; and FIG. 1
  • dysbiosis or a microbial imbalance, the severity of which is associated with disease severity; see Kong, H. H., et al. Genome research. 2012;22(5):850-859; and FIG. 1
  • FIG. 1 characterized by dysbiosis (or a microbial imbalance, the severity of which is associated with disease severity; see Kong, H. H., et al. Genome research. 2012;22(5):850-859; and FIG. 1), which is a notable feature of atopic dermatitis, and a lack of diversity of the skin microbiome, which is dominated by Staphylococcus aureus during atopic dermatitis flares and untreated skin.
  • Engineered probiotics are a novel approach based on leveraging the skin microbiome for therapeutic purposes.
  • an engineered probiotic has important advantages over other methods of drug delivery, as it will establish residence on the patient's skin and continuously and stably deliver therapeutic proteins in situ.
  • certain strains of Staphylococcus epidermidis (SE) have demonstrated important beneficial immunomodulatory and anti-pathogen effects in the skin, which are relevant to atopic dermatitis disease phenotype and severity.
  • SE Staphylococcus epidermidis
  • filaggrin which is a structural protein derived from profilaggrin, further enhances the therapeutic approach due to filaggrin' s role in the skin barrier and ability to reduce transepidermal water loss and improve skin hydration.
  • the present invention has the surprising advantage of providing methods and compositions for treating skin diseases, e.g., atopic dermatitis, using a genetically engineered, recombinant strain of Staphylococcus epidermidis as a skin drug delivery system that secretes human filaggrin to address the pathophysiology of atopic dermatitis ⁇ e.g., AZT-01).
  • skin diseases e.g., atopic dermatitis
  • a genetically engineered, recombinant strain of Staphylococcus epidermidis as a skin drug delivery system that secretes human filaggrin to address the pathophysiology of atopic dermatitis ⁇ e.g., AZT-01).
  • the benefits of this invention include its safety as a non-steroidal treatment option, its efficacy due to the invention's combination of benefits from the secretion of filaggrin along with the benefits of the topical application of Staphylococcus epidermidis, and its ability to be therapeutically effective at even a low frequency of application (no more than once a day).
  • the present invention therefore addresses the long-felt need for an effective treatment for inflammatory skin diseases, such as atopic dermatitis.
  • the present invention is also one of the first reported demonstrations of commensal skin bacteria that can secrete therapeutic proteins to treat skin disease.
  • the invention refers to methods and compositions for treating inflammatory skin diseases comprising, as an active principle, an engineered microorganism capable of expressing therapeutically relevant recombinant fusion polypeptides (i.e. proteins, peptides, or amino acids).
  • fusion polypeptides i.e. proteins, peptides, or amino acids.
  • the present invention features, in a first aspect, a recombinant microorganism capable of secreting a polypeptide, wherein the recombinant microorganism comprises an expression vector comprising a first coding sequence comprising a gene capable of expressing the polypeptide and a second coding sequence comprising a gene capable of expressing a cell penetrating peptide.
  • the recombinant microorganism further comprising a third coding sequence comprising a gene capable of expressing an export signal.
  • the expression of the first coding sequence, second coding sequence and third coding sequence is under the control of a promoter.
  • the arrangement of the first coding sequence, second coding sequence and third coding sequences are in- frame.
  • the first coding sequence, second coding sequence and third coding sequence are operably linked to a promoter.
  • the recombinant microorganism is bacteria, or a combination of bacteria.
  • the polypeptide is filaggrin, or a variant thereof.
  • the microorganism is selected from the group consisting of Bifidobacterium, Brevibacterium, Propionibacterium, Lactococcus, Streptococcus, Staphylococcus, Lactobacillus,
  • the recombinant microorganism is Staphylococcus epidermidis.
  • the microorganism secretes a filaggrin fusion protein.
  • the polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8 and SEQ ID NO: 9.
  • the polypeptide has at least about 80%, 81%, 82%, 83, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with SEQ ID NO: 1. In one embodiment, the polypeptide has at least about 80%, 81%, 82%, 83, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with SEQ ID NO: 2.
  • the polypeptide has at least about 80%, 81%, 82%, 83, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with SEQ ID NO: 3. In one embodiment, the polypeptide has at least about 80%, 81%, 82%, 83, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with SEQ ID NO: 4.
  • the polypeptide has at least about 80%, 81%, 82%, 83, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with SEQ ID NO: 5. In one embodiment, the polypeptide has at least about 80%, 81%, 82%, 83, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with SEQ ID NO: 6.
  • the polypeptide has at least about 80%, 81%, 82%, 83, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with SEQ ID NO: 7. In one embodiment, the polypeptide has at least about 80%, 81%, 82%, 83, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with SEQ ID NO: 8.
  • the polypeptide has at least about 80%, 81%, 82%, 83, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with SEQ ID NO: 9.
  • the present invention features, in a further aspect, a method for producing a live biotherapeutic composition, the method comprising (a) transfecting a cell with (i) a first coding sequence comprising a nucleic acid sequence capable of expressing a therapeutic polypeptide, and (ii) a second coding sequence comprising a nucleic acid sequence capable of expressing a cell penetrating peptide; and (b) allowing the transfected cell to produce a therapeutic polypeptide fusion protein; and (c) obtaining the live biotherapeutic composition.
  • the method further comprises (iii) transfecting the cell with a third coding sequence comprising a nucleic acid sequence capable of expressing an export signal.
  • first coding sequence, second coding sequence and third coding sequences are arranged in a single plasmid.
  • the arrangement of the first coding sequence, second coding sequence and third coding sequences are operably linked to a promoter.
  • the cell is selected from the group consisting of wherein the microorganism is selected from the group consisting of Bifidobacterium, Brevibacterium, Propionibacterium, Lactococcus, Streptococcus, Staphylococcus,
  • the cell is Staphylococcus epidermidis.
  • the therapeutic polypeptide fusion protein is a filaggrin fusion protein, or a variant thereof.
  • the present invention features, in another aspect, a nucleic acid comprising a nucleic acid sequence encoding a polypeptide as set forth any one of the aspects or embodiments herein.
  • the present invention features, in a further aspect, a composition obtained by any one of the method disclosed or described herein.
  • the composition comprises a pharmaceutically acceptable carrier, wherein the pharmaceutically acceptable carrier is selected from the group consisting of an aqueous solution, an emulsion, a cream, a lotion, a gel, or an ointment.
  • a live biotherapeutic composition comprising a recombinant microorganism wherein the recombinant microorganism comprises (i) a first coding sequence comprising a nucleic acid sequence capable of expressing a therapeutic polypeptide; (ii) a second coding sequence comprising a nucleic acid sequence capable of expressing a cell penetrating peptide; (iii) a third coding sequence comprising a nucleic acid sequence capable of expressing an export signal; and (iiv) a promoter operably linked to the first coding sequence, the second coding sequence and the third coding sequence; wherein the first coding sequence, second coding sequence and first coding sequence is capable of expressing a filaggrin fusion product, or variant thereof.
  • the recombinant microorganism is Staphylococcus epidermidis.
  • the export signal exports the filaggrin fusion product, or variant thereof, out of the recombinant microorganism.
  • the cell penetrating peptide facilitates the entry of the filaggrin fusion product, or variant thereof, into a human keratinocyte.
  • the composition comprises a pharmaceutically acceptable carrier, wherein the pharmaceutically acceptable carrier is selected from the group consisting of an aqueous solution, an emulsion, a cream, a lotion, a gel, or an ointment.
  • the present invention features, in a further aspect, a kit comprising any one of the compositions disclosed or described herein and instructions for use.
  • the present invention features, in a further aspect, a method of treating a skin disease comprising administering to a subject in need thereof the composition of any one of the compositions disclosed or described herein.
  • the skin disease is atopic dermatitis.
  • FIG. 1A-F depicts the relationship between staphylococcal species and atopic dermatitis.
  • FIG. IB shows proportion of S. aureus and Shannon diversity index in AcPc. Partial correlation (adjusting for disease state, AcPc).
  • FIG. 1C shows longitudinal trend of mean proportion of S. epidermidis in AcPc.
  • FIG. ID shows correlation of proportion of S. aureus versus objective SCORAD for each site (AcPc, Volar forearm [Vf], Nares [N]).
  • FIG. IF atopic dermatitis microbiome progression hypothesis. (*) Proposed relationship among shifts in skin microbial diversity, the proportion of
  • FIG. 2A depicts a schematic drawing of a Staphylococcus epidermidis-based protein delivery system, as described herein.
  • the construct design comprises a promoter, a ribosome binding site (RBS), an export signal, a filaggrin expression sequence, and a cell-penetrating peptide sequence.
  • FIG. 2B displays the characterization of certain promoters for tunable control of protein expression (using GFP as a reporter).
  • FIG 2C shows characterization of export signals for protein export out of SE (GFP used as reporter).
  • FIG. 2D shows Western blot analysis of human filaggrin produced from Staphylococcus epidermidis, mouse filaggrin produced from Staphylococcus epidermidis, and whole mouse skin (anti-mouse flaggrin antibodies were used).
  • FIG. 3A-3D depicts the characterization of GFP-producing Staphylococcus epidermidis in reconstituted human epidermis (RHE).
  • FIG.3A shows fluorescence and light wavelength overlays of RHE at ⁇ 25 ⁇ m at two hours past application of Staphylococcus epidermidis-GFP .
  • FIG. 3B-3D shows fluorescence and light wavelength overlays of RHE two hours after dermaroller application then topical Staphylococcus epidermidis-GFP application. Depths taken at 0 ⁇ m FIG. 3B, 50 ⁇ . 3C, and 70 ⁇ m FIG. 3D.
  • FIG. 4A-4E depicts the characterization of SE-GFP colonization in mice.
  • FIG. 4A-4C shows in vivo two-photon microscopy of mouse skin three days following treatment of GFP- expressing S. epidermidis.
  • FIG. 4D Light microscopy of dorsal skin of mice following SE-GFP application.
  • FIG. 4E Light microscopy of dorsal skin of mice following SE-GFP application.
  • FIG. 5A-5K depicts the characterization of protein with and without the RMR signal using 50 ⁇ g GFP as a reporter in RHE.
  • FIG. 5A-5D show two-photon images of topically applied GFP with (FIG. 5C, FIG. 5D) or without (FIG. 5A, FIG. 5B) the RMR signal at 30 minutes (FIG. 5 A, FIG. 5C, FIG. 5E, FIG. 5G) or 60 minutes (FIG. 5B, FIG. 5D, FIG. 5F, FIG. 5H). Images are compiled Z-stacks projected onto a 2D plane. (FIG. 5E-FIG. 5H) 3D surface analysis to examine depth of protein penetration into the RHE. (FIG. 5I-FIG. 5N) Confocal images of GFP (FIG. 5K, FIG. N), GFP + RMR (FIG. 5J, FIG. 5M) or vehicle (FIG. 51, FIG. 5L) using light (FIG. 5L-FIG. 5N) or fluorescent (FIG. 5I-FIG. 5K) wavelengths.
  • FIG. 6 depicts the experimental outline of 16S rRNA sequencing.
  • FIG. 7 is a graph that shows hydrophobicity score as a function of amino acid position for the entire human filaggrin (hFLG) sequence (Uniprot P20930).
  • FIG. 8 is a graph that shows hydrophobicity score as a function of amino acid position for the entire mouse filaggrin (mFLG) sequence (NCBI Reference Sequence:
  • FIG. 9 is a graph that shows hydrophobicity score as a function of amino acid position for the hFLG region starting at amino acid 1400 to 1800 with the unit segment of domains 9 and 10.
  • FIG. 10 is a graph that shows hydrophobicity score as a function of amino acid position for hFLG[9-10](1429-1774) from amino acid position 1400 to amino acid position 1800 in hFLG.
  • FIG. 11 is a graph that shows hydrophobicity score as a function of amino acid position for the start and end positions of the hFLG [9-10] (1429-1777).
  • FIG. 12 is a graph that shows hydrophobicity score as a function of amino acid position from a point of low hydrophobicity to the next point of low hydrophobicity
  • FIG. 13 shows an alignment of human filaggrin dimers hFLG[3-4], hFLG[5-6], hFLG[7-8], hFLG[9-10], hFLG[l l-12], hFLG[13-14], hFLG[15-16], hFLG[17-18], hFLG[ 19-20], hFLG[21-22].
  • FIG. 14 is a graph that shows background FLG binding at ⁇ g/well for 2h at 37°C
  • FIG. 15 is a graph that shows binding of hFLG segments to human callus keratin (NSB removed).
  • FIG. 16 is a graph that shows titration of IgY anti-hFLG. Detailed Description of the Invention
  • an element means one element or more than one element.
  • abnormal skin condition or a “skin disease” refers to a skin state or condition that is generally undesirable or deleterious compared to the normal or baseline condition of human skin.
  • abnormal skin conditions include: psoriasis, acne, atopic dermatitis, allergic contact dermatitis, epidermolytic hyperkeratosis, seborrheic dermatitis, eczema, dry skin, allergy, rashes, UV-irritated skin, detergent irritated skin (including irritation caused by enzymes and molecules used in washing detergents and sodium lauryl sulfate), thinning skin (e.g. skin from the elderly and children), bullous pemphigoid, pemphigus vulgaris, impetigo, vitiligio, baldness, and hirsutism.
  • the terms "patient” or “subject”, refers to a human or animal (in the case of an animal, more typically a mammal such as domesticated mammals, or animals such as poultry animals and fish and other seafood or freshwater food creatures), that would be subjected to the treatments and compositions of the present invention. Such patient or subject would be considered to be in need of the pharmaceutical compositions of the present invention or of the methods of treating, preventing, or reducing the risk of an abnormal skin condition or a skin disease (e.g., an inflammatory skin disease).
  • a skin disease e.g., an inflammatory skin disease
  • the term "therapeutically effective amount” refers to an amount of a pharmaceutical active compound, a live biotherapeutic composition, a combination of compounds or compositions, or an amount of pharmaceutical active compound delivered by an engineered bacterial strain or strains, for example a skin treatment agent or agents, when administered alone or in combination, to treat, prevent, or reduce the risk of a disease state or condition, for example an abnormal skin condition or a skin disease (e.g., an inflammatory skin disease).
  • the term also refers to an amount of a pharmaceutical composition containing an active compound or combination of compounds or an engineered bacterial strain or strains that delivers a pharmaceutical active compound.
  • an effective amount refers to an amount of the compound or an amount of the compound delivered by an engineered bacterial strain (or a recombinant bacterial strain) or strains present in a formulation given to a recipient patient or subject sufficient to elicit biological activity, for example, activity for treating or preventing an abnormal skin condition or a skin disease (e.g., an inflammatory skin disease).
  • an engineered bacterial strain or a recombinant bacterial strain
  • a formulation for example, activity for treating or preventing an abnormal skin condition or a skin disease (e.g., an inflammatory skin disease).
  • the phrase "pharmaceutically acceptable” refers to those active compounds, materials, engineered bacterial strain or strains, compositions, carriers, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problems or complications, commensurate with a reasonable benefit/risk ratio.
  • the term “treating” refers to providing a therapeutic intervention to cure or ameliorate an abnormal skin condition.
  • preventing refers to completely or almost completely stopping an abnormal skin condition from occurring, for example when the patient or subject is predisposed to an abnormal skin condition or at risk of contracting an abnormal skin condition. Preventing can also include inhibiting, i.e. arresting the development, of an abnormal skin condition.
  • reducing the risk of refers to lowering the likelihood or probability of an abnormal skin condition from occurring, for example when the patient or subject is predisposed to an abnormal skin condition or at risk of contracting an abnormal skin condition.
  • the term "engineered bacterial strain,” or a “recombinant bacterial strain” refers to a strain of bacteria that has been "genetically modified” or “engineered” by the introduction of DNA prepared outside the organism into the bacterial strain.
  • the introduction of a plasmid containing new genes or other nucleic acid sequence(s) into bacteria will allow the bacteria to express those genes or other nucleic acid sequence(s).
  • the plasmid containing new genes or other nucleic acid sequence(s) can be introduced to the bacteria and then integrated into the bacteria's genome, where the bacteria will express those genes or other nucleic acid sequence(s).
  • carriers refer to compatible substances that are suitable for delivering, containing, or “carrying” a pharmaceutical active ingredient or other materials for administration in a topically applied composition to a patient or subject.
  • Carriers useful herein should be pharmaceutically acceptable. Carriers and vehicles useful herein include any such materials known in the art, which are non-toxic and do not interact with other components of the formulation in which it is contained in a deleterious manner.
  • aqueous refers to a formulation that contains water or that becomes water-containing following application to the skin or mucosal tissue.
  • carriers include water, lower alcohols, higher alcohols, polyhydric alcohols, monosaccharides, disaccharides, polysaccharides, hydrocarbon oils, fats and oils, waxes, fatty acids, silicone oils, nonionic surfactants, ionic surfactants, silicone surfactants, and water- based mixtures and emulsion-based mixtures of such carriers.
  • polypeptide or "protein” refer to biological molecules, or macromolecules composed of amino-acid residues bonding together in a chain.
  • the definition of polypeptides used herein is intended to encompass proteins (generally higher molecular weight) composed of one or more long chains of amino acid residues and small peptides (generally lower molecular weight) of a few amino acids. In other embodiments, a single amino acid, although not technically a polypeptide, is also considered within the scope of the invention.
  • live biotherapeutic product refers to a product candidate(s) containing bacteria, yeast, and/or other microorganisms.
  • isolated designates a biological material (cell, nucleic acid or protein) that has been removed from its original environment (the environment in which it is naturally present).
  • a polynucleotide present in the natural state in a plant or an animal is not isolated, however the same polynucleotide separated from the adjacent nucleic acids in which it is naturally present, is considered “isolated.”
  • an "isolated nucleic acid molecule” (such as, for example, an isolated promoter) is one which is separated from other nucleic acid molecules which are present in the natural source of the nucleic acid.
  • isolated nucleic acid molecule includes nucleic acid molecules which are separated from the chromosome with which the genomic DNA is naturally associated.
  • an “isolated” nucleic acid molecule is free of sequences which naturally flank the nucleic acid molecule in the genomic DNA of the organism from which the nucleic acid molecule is derived.
  • the present invention provides skin-colonizing bacteria that are genetically altered to express recombinant therapeutic polypeptides for the treatment or prevention of skin disease (FIG. 2).
  • Using genetically engineered protein-producing bacteria has several advantages over the prior art method of treating skin disease.
  • Therapeutic proteins are able to treat the underlying cause of defects leading to the skin condition. Further, bacteria are able to self- replicate while retaining the inserted gene to continuously produce the therapeutic protein.
  • the present invention provides skin-colonizing bacteria, such as for example, Staphylococcus epidermidis, that are genetically altered to express human filaggrin.
  • skin-colonizing bacteria such as for example, Staphylococcus epidermidis
  • Using genetically engineered filaggrin-producing bacteria has several advantages over using filaggrin supplementation.
  • bacteria are able to self-replicate while retaining the inserted filaggrin gene.
  • S. epidermidis is normally present on the skin and has been shown to inhibit growth of Staphylococcus aureus, a bacterial species of the same genre that dominates the skin flora in AD flares.
  • the present invention provides skin-colonizing microorganisms, e.g., bacteria, that are genetically altered to express recombinant therapeutic polypeptides for the treatment or prevention of skin disease (FIG. 2).
  • skin-colonizing microorganisms e.g., bacteria
  • Using genetically engineered protein-producing microorganisms, e.g., bacteria has several advantages over the prior art method of treating skin disease.
  • Therapeutic proteins are able to treat the underlying cause of defects leading to the skin condition.
  • microorganisms, e.g., bacteria are able to self-replicate while retaining the inserted nucleic acid (e.g., a gene) to continuously produce the therapeutic protein.
  • the present invention provides skin-colonizing microorganisms, e.g., bacteria, such as for example, Staphylococcus epidermidis, that are genetically altered to express therapeutic proteins, e.g., human filaggrin.
  • skin-colonizing microorganisms e.g., bacteria, such as for example, Staphylococcus epidermidis
  • therapeutic proteins e.g., human filaggrin.
  • microorganisms e.g., bacteria
  • microorganisms e.g., bacteria
  • S. epidermidis is normally present on the skin and has been shown to inhibit growth of Staphylococcus aureus, a bacterial species of the same genre that dominates the skin flora in atopic dermatitis flares.
  • Bacterial Strains Bacterial Strains
  • the present invention provides genetically altered microorganisms, e.g., bacteria, capable of expressing recombinant therapeutic proteins.
  • a wide range of microorganisms are suitable for use in the present invention. Examples include, but are not limited to, nonpathogenic and commensal bacteria.
  • Bacteria suitable for use in the present invention include, but are not limited to, Bifidobacterium, Brevibacterium, Propionibacterium, Lactococcus, Streptococcus, Staphylococcus (e.g., S. epidermidis), Lactobacillus (e.g., L. acidophilus), Pediococcus, Leuconostoc, or Oenococcus.
  • the bacterium is Staphylococcus epidermidis.
  • the strain of S. epidermidis to be used is incapable of producing biofilms.
  • One such example of a strain of S. epidermidis incapable of producing biofilms is S. epidermidis strain ATCC 12228.
  • other related or similar species found on the skin can be used.
  • the present invention provides genetically altered microorganisms, e.g., bacteria, capable of expressing recombinant therapeutic proteins.
  • the disclosure is directed to therapeutic proteins that include a filaggrin polypeptide amino acid sequence. In some embodiments, the disclosure is directed to therapeutic proteins that include a filaggrin polypeptide amino acid sequence and a cell penetrating polypeptide amino acid sequence. In some embodiments, the disclosure is directed to therapeutic proteins that include a filaggrin polypeptide amino acid sequence, a cell penetrating polypeptide amino acid sequence and a secretion signal or export signal polypeptide sequence.
  • a "polypeptide” generally is defined herein to refer to a peptide sequence of about 2 to about 10,000 or more amino acid residues.
  • amino acid not only encompasses the 20 common amino acids in naturally synthesized proteins, but also includes any modified, unusual, or synthetic amino acid. One of ordinary skill in the art would be familiar with modified, unusual, or synthetic amino acids.
  • polypeptides of the present invention may possess deletions and/or substitutions of amino acids relative to the native sequence; thus, sequences with a deletion, sequences with a substitution, and sequences with a deletion and a substitution are contemplated for inclusion in the polypeptides of the present invention.
  • these polypeptides may further include insertions or added amino acids, such as linkers.
  • Substitutional or replacement variants typically contain the exchange of one amino acid for another at one or more sites within the protein and may be designed to modulate one or more properties of the polypeptide, particularly to increase its efficacy or specificity. Substitutions of this kind preferably are conservative, that is, one amino acid is replaced with one of similar shape and charge.
  • Conservative substitutions are well known in the art and include, for example, the changes of: alanine to serine; arginine to lysine; asparagine to glutamine or histidine; aspartate to glutamate; cysteine to serine; glutamine to asparagine; glutamate to aspartate; glycine to proline; histidine to asparagine or glutamine; isoleucine to leucine or valine; leucine to valine or isoleucine; lysine to arginine; methionine to leucine or isoleucine; phenylalanine to tyrosine, leucine or methionine; serine to threonine; threonine to serine; tryptophan to tyrosine; tyrosine to tryptophan or phenylalanine; and valine to isoleucine or leucine.
  • polypeptides may possess an insertion one or more residues. This may include the addition of one or more amino acid residues.
  • Amino acid substitutions generally are based on the relative similarity of the amino acid side-chain substituents, for example, their hydrophobicity, hydrophilicity, charge, size, and the like.
  • Exemplary substitutions that take into consideration the various foregoing characteristics are well known to those of skill in the art and include: arginine and lysine; glutamate and aspartate; serine and threonine; glutamine and asparagine; and valine, leucine and isoleucine.
  • the disclosure is directed to therapeutic proteins that include a filaggrin polypeptide amino acid sequence.
  • the therapeutic protein comprises human filaggrin.
  • Human filaggrin is expressed by a human gene encoding filaggrin (FLG).
  • FLG human gene encoding filaggrin
  • keratinocytes and functions to aggregate keratin filaments into a cytoskeleton, which, in combination with other components, comprises the cornified cell envelope.
  • FLG is a large gene located on chromosome lq21 that produces profilaggrin, an insoluble polyprotein that is proteolyzed to release functional filaggrin monomers (Armengot-Carbo et al. 2014).
  • the therapeutic protein (and, i.e., the gene from which the protein is expressed) of the invention may be from any mammal. Non- limiting examples include, but are not limited to, mouse, rat, rabbit, goat, sheep, horse, cow, dog, primate, or human gene sequence.
  • the filaggrin amino acid sequences contemplated for inclusion in the polypeptides, compositions, and methods of the present invention may be obtained from any source.
  • the filaggrin amino acid may be obtained from a natural source or may be chemically synthesized.
  • the filaggrin amino acid sequence may be from any species.
  • it may be a mammalian filaggrin amino acid sequence.
  • Non-limiting examples include mouse, rat, rabbit, goat, sheep, horse, cow, dog, cat, primate, or human amino acid sequence.
  • the filaggrin amino acid sequence is a human amino acid sequence.
  • Non- limiting examples of filaggrin proteins are set forth in Table 1, below.
  • the filaggrin amino acid sequence includes any of the amino acid sequences set forth in Table 1.
  • the filaggrin amino acid sequence includes Gen Bank Accession No. NP_002007.1 (SEQ ID NO: l).
  • the filaggrin amino acid sequence includes 20, 30, 40, 50, 60, 70, 80, 90, 100, 120, 130, 150, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340 or more consecutive amino acids of any of the amino acid sequences set forth in Table 1, or any range of amino acids derivable therein, so long as the filaggrin amino acid sequence when conjugated to a cell penetrating peptide and/or export or secretion signal retains at least some of the function of a native filaggrin amino acid sequence conjugated to the same cell penetration peptide and/or export or secretion signal.
  • the filaggrin amino acid sequence has at least about 80%, 81%, 82%, 83, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with a native filaggrin amino acid sequence, or any range of percent sequence identify derivable therein.
  • the filaggrin amino acid sequence is an amino acid sequence selected from Table 1.
  • the filaggrin amino acid sequence has at least about 80%, 81%, 82%, 83, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with SEQ ID NO: 1.
  • the filaggrin amino acid sequence has at least about 80%, 81%, 82%, 83, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with SEQ ID NO: 2.
  • the filaggrin amino acid sequence has at least about 80%, 81%, 82%, 83, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with SEQ ID NO: 3.
  • the filaggrin amino acid sequence has at least about 80%, 81%,
  • the filaggrin amino acid sequence has at least about 80%, 81%, 82%, 83, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with SEQ ID NO: 5.
  • the filaggrin amino acid sequence has at least about 80%, 81%, 82%, 83, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with SEQ ID NO: 6. In some embodiments, the filaggrin amino acid sequence has at least about 80%, 81%, 82%, 83, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with SEQ ID NO: 7.
  • the filaggrin amino acid sequence has at least about 80%, 81%, 82%, 83, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with SEQ ID NO: 8.
  • the human filaggrin consensus sequence is a consensus sequence shown as SEQ ID NO: 9, and refers to a sequence formed from the most frequently occurring amino acids in hFLG[3-4], hFLG[5-6], hFLG[7-8], hFLG[9-10], hFLG[l l-12], hFLG[13-14], hFLG[15-16], hFLG[17-18], hFLG[19-20], hFLG[21-22].
  • the filaggrin amino acid sequence has at least about 80%, 81%, 82%, 83, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with SEQ ID NO: 9.
  • sequence identity is defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues at corresponding positions in a native polypeptide sequence, after aligning the sequences and introducing gaps if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity.
  • the % sequence identity values may be generated by the NCBI BLAST2.0 software as defined by Altschul et al. (1997). The parameters are set to default values, with the exception of Penalty for mismatch, which is set to -1.
  • the therapeutic protein comprises a recombinant fusion protein comprising filaggrin operably linked to a cell penetrating protein (CPP).
  • CPP cell penetrating protein
  • the therapeutic protein comprises a
  • the therapeutic protein comprises a recombinant fusion protein comprising filaggrin operably linked to a cell penetrating protein (CPP) and to an export or secretion signal.
  • CPP cell penetrating protein
  • polypeptides set forth herein may comprises a sequence of any number of additional amino acid residues at either the N-terminus or C-terminus of the amino acid sequence that includes the filaggrin amino acid sequence and the cell penetrating protein (CPP) and/or export or secretion signal.
  • CPP cell penetrating protein
  • Secretion signals or export signals are peptide sequences on a protein that facilitate the export of the protein through the secretory pathway, which ultimately results in the protein being secreted from the cell.
  • any secretion signal that facilitates the export of a protein such as a protein comprising filaggrin, out of a
  • microorganism e.g., a bacterial cell
  • a secretion signal e.g., a secretion signal
  • a cell penetrating peptide is a peptide sequence that facilitates or mediates the delivery of a biomolecule (e.g., a protein) in vivo without using any receptors and without causing any significant membrane damage.
  • a biomolecule e.g., a protein
  • Cell penetrating peptides that facilitate entry into the skin keratinocytes are contemplated as a cell penetrating peptides of the present invention.
  • the present disclosure provides a recombinant microorganism capable of secreting a polypeptide, wherein the recombinant microorganism comprises an expression vector comprising a first coding sequence comprising a gene capable of expressing the polypeptide and a second coding sequence comprising a gene capable of expressing a cell penetrating peptide, where the polypeptide comprises a filaggrin
  • the present disclosure provides a recombinant microorganism capable of secreting a polypeptide, wherein the recombinant microorganism comprises an expression vector comprising a first coding sequence comprising a gene capable of expressing the polypeptide and a second coding sequence comprising a gene capable of expressing a cell penetrating peptide, where the polypeptide comprises an amino acid sequence at least 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 1.
  • the present disclosure provides a recombinant microorganism capable of secreting a polypeptide, wherein the recombinant microorganism comprises an expression vector comprising a first coding sequence comprising a gene capable of expressing the polypeptide and a second coding sequence comprising a gene capable of expressing a cell penetrating peptide, where the polypeptide comprises an amino acid sequence at least 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 2.
  • the present disclosure provides a recombinant microorganism capable of secreting a polypeptide, wherein the recombinant microorganism comprises an expression vector comprising a first coding sequence comprising a gene capable of expressing the polypeptide and a second coding sequence comprising a gene capable of expressing a cell penetrating peptide, where the polypeptide comprises an amino acid sequence at least 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 3.
  • the present disclosure provides a recombinant microorganism capable of secreting a polypeptide, wherein the recombinant microorganism comprises an expression vector comprising a first coding sequence comprising a gene capable of expressing the polypeptide and a second coding sequence comprising a gene capable of expressing a cell penetrating peptide, where the polypeptide comprises an amino acid sequence at least 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 4.
  • the present disclosure provides a recombinant microorganism capable of secreting a polypeptide, wherein the recombinant microorganism comprises an expression vector comprising a first coding sequence comprising a gene capable of expressing the polypeptide and a second coding sequence comprising a gene capable of expressing a cell penetrating peptide, where the polypeptide comprises an amino acid sequence at least 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 5.
  • the present disclosure provides a recombinant microorganism capable of secreting a polypeptide, wherein the recombinant microorganism comprises an expression vector comprising a first coding sequence comprising a gene capable of expressing the polypeptide and a second coding sequence comprising a gene capable of expressing a cell penetrating peptide, where the polypeptide comprises an amino acid sequence at least 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 6.
  • the present disclosure provides a recombinant microorganism capable of secreting a polypeptide, wherein the recombinant microorganism comprises an expression vector comprising a first coding sequence comprising a gene capable of expressing the polypeptide and a second coding sequence comprising a gene capable of expressing a cell penetrating peptide, where the polypeptide comprises an amino acid sequence at least 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 7.
  • the present disclosure provides a recombinant microorganism capable of secreting a polypeptide, wherein the recombinant microorganism comprises an expression vector comprising a first coding sequence comprising a gene capable of expressing the polypeptide and a second coding sequence comprising a gene capable of expressing a cell penetrating peptide, where the polypeptide comprises an amino acid sequence at least 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 8.
  • the present disclosure provides a recombinant microorganism capable of secreting a polypeptide, wherein the recombinant microorganism comprises an expression vector comprising a first coding sequence comprising a gene capable of expressing the polypeptide and a second coding sequence comprising a gene capable of expressing a cell penetrating peptide, where the polypeptide comprises an amino acid sequence at least 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 9.
  • the present disclosure provides a recombinant microorganism capable of secreting a polypeptide, wherein the recombinant microorganism comprises an expression vector comprising an amino acid sequence at least 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 2.
  • the present disclosure provides a recombinant microorganism capable of secreting a polypeptide, wherein the recombinant microorganism comprises an expression vector comprising an amino acid sequence at least 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 3.
  • the present disclosure provides a recombinant microorganism capable of secreting a polypeptide, wherein the recombinant microorganism comprises an expression vector comprising an amino acid sequence at least 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 4.
  • the present disclosure provides a recombinant microorganism capable of secreting a polypeptide, wherein the recombinant microorganism comprises an expression vector comprising an amino acid sequence at least 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 5.
  • the present disclosure provides a recombinant microorganism capable of secreting a polypeptide, wherein the recombinant microorganism comprises an expression vector comprising an amino acid sequence at least 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 6.
  • the present disclosure provides a recombinant microorganism capable of secreting a polypeptide, wherein the recombinant microorganism comprises an expression vector comprising an amino acid sequence at least 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 7.
  • the present disclosure provides a recombinant microorganism capable of secreting a polypeptide, wherein the recombinant microorganism comprises an expression vector comprising an amino acid sequence at least 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 8.
  • the present invention includes nucleic acids that include a nucleic acid sequence that encodes a recombinant polypeptide of the present invention. Some embodiments of the present invention include a nucleic acid that includes a nucleic acid sequence that encodes a polypeptide as set forth above. Further embodiments include a nucleic acid that encodes a filaggrin amino acid sequence. The filaggrin amino acid sequence is any filaggrin amino acid sequence as set forth herein. In some embodiments, the nucleic acid is comprised in an expression vector. The term "nucleic acid" is well known in the art.
  • nucleic acid as used herein will generally refer to a molecule (i.e., a strand) of DNA, RNA or a derivative or analog thereof, comprising a nucleobase.
  • a nucleobase includes, for example, a naturally occurring purine or pyrimidine base found in DNA (e.g., an adenine "A,” a guanine “G,” a thymine “T” or a cytosine “C”) or RNA (e.g., an A, a G, an uracil "U” or a C).
  • nucleic acid encompass the terms “oligonucleotide” and “polynucleotide,” each as a subgenus of the term “nucleic acid.”
  • oligonucleotide refers to a molecule of between 3 and about 100 nucleobases in length.
  • polynucleotide refers to at least one molecule of greater than about 100 nucleobases in length. These definitions refer to a single- stranded or double- stranded nucleic acid molecule. Double stranded nucleic acids are formed by fully complementary binding, although in some embodiments a double stranded nucleic acid may formed by partial or substantial complementary binding.
  • a nucleic acid may encompass a double- stranded molecule that comprises one or more complementary strand(s) or "complement(s)" of a particular sequence, typically comprising a molecule.
  • a single stranded nucleic acid may be denoted by the prefix "ss” and a double stranded nucleic acid by the prefix "ds”.
  • the present invention utilizes standard molecular biology techniques, e.g., those described in (Sambrook et al. 2001).
  • An example of the genetic construct used for this invention is pAZT, which is based on pJB38, an allelic exchange E. coli-staphylococcal shuttle vector, further comprising additional design features on the plasmid to improve functionality (Bose, J.L., et al. Applied and environmental microbiology. 2013;79(7):2218- 2224).
  • the plasmid is constructed by inserting cDNA of a gene encoding a therapeutic protein into a restriction site , using standard molecular biology techniques (FIG. 2).
  • the insert further comprises a coding sequence driven by a promoter.
  • a promoter can be either constitutive or inducible. Examples of inducible promoters include those that are activated by chemical compounds such as alcohols, sugars, metals, or tetracycline, or by physical factors such as light or high temperatures
  • the mRNA sequence of human FLG has a Genebank accession No. NM_002016.
  • a plasmid pAZT was constructed by inserting part of the FLG cDNA into a restriction site of pJB38.
  • the insert contains a nucleic acid coding sequence driven by a promoter.
  • the construct further comprises a nucleic acid sequence encoding a secretion signal and a cell penetrating peptide, thus resulting in a recombinant filaggrin fusion protein.
  • the skin disease to be treated can be any disease or disorder associated with skin.
  • the disorder is selected from the group consisting of atopic dermatitis, psoriasis, acne, allergic contact dermatitis, epidermolytic hyperkeratosis, seborrheic dermatitis, eczema, dry skin, allergy, rashes, UV-irritated skin, detergent irritated skin (including irritation caused by enzymes and compounds used in washing detergents and sodium lauryl sulfate), thinning skin (e.g.
  • proteins that can be administered according to the invention are preferably eukaryotic proteins. These proteins include, but are not limited to, single amino acids, small peptides, and large proteins.
  • genes encoding proteins that are useful in the invention as recombinant therapeutic proteins include, but are not limited to, the following: members of the interleukin family of genes, including, but not limited to, IL-2, IL- 3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, IL-13, IL-14 and IL-15 and genes encoding receptor antagonists thereof.
  • Genes which encode hematopoietic growth factors including but not limited to, erythropoietin, granulocyte colony stimulating factor, granulocyte macrophage colony stimulating factor, macrophage colony stimulating factor, stem cell factor, leukemia inhibitory factor and thrombopoietin are also contemplated in the invention.
  • Genes encoding neurotropic factors are also contemplated, including but not limited to, nerve growth factor, brain derived neurotropic factor and ciliary neurotropic factor.
  • genes which encode interferons including, but not limited, to IFN-alpha, IFN-beta and IFN-gamma are included.
  • genes encoding chemokines such as the C-C family and the C-X-C family of cytokines
  • genes encoding hormones such as proinsulin and growth hormone
  • tissue plasminogen activator including tissue plasminogen activator, streptokinase, urokinase or other enzymes such as trypsin inhibitor.
  • the invention further includes genes which encode tissue repair factors, growth and regulatory factors including, but not limited to, oncostatine M, platelet-derived growth factors, fibroblast growth factors, epidermal growth factor, hepatocyte growth factor, bone morphogenic proteins, insulin-like growth factors, calcitonin and transforming growth factor alpha and beta.
  • tissue repair factors including, but not limited to, oncostatine M, platelet-derived growth factors, fibroblast growth factors, epidermal growth factor, hepatocyte growth factor, bone morphogenic proteins, insulin-like growth factors, calcitonin and transforming growth factor alpha and beta.
  • Further contemplated genes include genes encoding structural proteins including filaggrin, actin, collagen, fibrillin, elastin, or scleroprotein.
  • microorganism e.g., bacteria
  • a therapeutically effective amount of a desired polypeptide for example, at least about 0.01%, about 0.05%, about 0.1%, about 0.2%, about 0.3%, about 0.4%, about 0.5%, about 0.6%, about 0.7%, about 0.8%, about 0.9%, about 1.0%, about.
  • the formulation for use according to the present invention can comprise, for example, at least about 0,01% to about 30%, about 0.01% to about 20%, about 0.01% to about 5%, about 0.1 % to about 30%, about 0.1% to about 20%, about 0.1% to about 15%, about 0.1 % to about 10%, about 0.1% to about 5%, about 0.2% to about 5%, about 0,3% to about 5%, about 0.4% to about 5%, about 0.5% to about 5%, about 1% to about 5%, or more by weight of a genetically engineered microorganism, e.g., bacteria.
  • a genetically engineered microorganism e.g., bacteria.
  • the topical formulation for use in the present invention can be in any form suitable for application to the body surface, such as a cream, lotion, sprays, solution, gel, ointment, paste, plaster, paint, bioadhesive, suspensions, emulsions, or the like, and/or can be prepared so as to contain liposomes, micelles, and/or microspheres.
  • a formulation can be used in combination with an occlusive overlayer so that moisture evaporating from the body surface is maintained within the formulation upon application to the body surface and thereafter.
  • the formulation can include a living bio therapeutic composition and can comprise at least one a genetically engineered microorganism, e.g., an engineered bacterial strain, that produces a recombinant polypeptide.
  • This engineered living biotherapeutic composition can deliver the polypeptide directly to the skin for treating or preventing abnormal skin conditions, and/or skin diseases (e.g., inflammatory skin diseases).
  • Topical formulations include those in which any other active ingredients are dissolved or dispersed in a dermatological vehicle known in the art, e.g. aqueous or nonaqueous gels, ointments, water-in-oil or oil-in-water emulsions.
  • Constituents of such vehicles may comprise water, aqueous buffer solutions, non-aqueous solvents (such as ethanol, isopropanol, benzyl alcohol, 2-(2-ethoxyethoxy)ethanol, propylene glycol, propylene glycol monolaurate, glycofurol or glycerol), oils (e.g. a mineral oil such as a liquid paraffin, natural or synthetic triglycerides such as MIGLYOL, or silicone oils such as dimethicone).
  • a dermatological vehicle known in the art, e.g. aqueous or nonaqueous gels, ointments, water-in-oil or oil-in-water emulsions.
  • dermatological vehicle employed can contain one or more components (e.g., when the formulation is an aqueous gel, components in addition to water) selected from the following: a solubilizing agent or solvent (e.g. a ⁇ -cyclodextrin, such as bydroxypropyl ⁇ - cyclodextrin, or an alcohol or polyol such as ethanol, propylene glycol or glycerol); a thickening agent (e.g. hydroxyethylceliulose, hydroxypropylcellulose, carboxymethylcellulose or carbomer); a gelling agent (e.g. a polyoxyethylene-polyoxypropylene copolymer); a preservative (e.g.
  • a solubilizing agent or solvent e.g. a ⁇ -cyclodextrin, such as bydroxypropyl ⁇ - cyclodextrin, or an alcohol or polyol such as ethanol, propylene glycol or glycerol
  • benzyl alcohol benzalkonium chloride, chlorhexidine, chlorbutol, a benzoate, potassium sorbate or EDTA or salt thereof
  • pH buffering agent(s) such as a mixture of dihydrogen phosphate and hydrogen phosphate salts, or a mixture of citric acid and a hydrogen phosphate salt.
  • a pharmaceutically acceptable carrier can also be incorporated in the formulation of the present invention and can be any carrier conventionally used in the art. Examples thereof include water, lower alcohols, higher alcohols, polyhydric alcohols, monosaccharides, disaccharides, polysaccharides, hydrocarbon oils, fats and oils, waxes, fatty acids, silicone oils, nonionic surfactants, ionic surfactants, silicone surfactants, and water- based mixtures and emulsion-based mixtures of such carriers.
  • pharmaceutically acceptable or “pharmaceutically acceptable carrier” is used herein to refer to a compound or composition that can be incorporated into a pharmaceutical formulation without causing undesirable biological effects or unwanted, interaction with other components of the formulation
  • carriers or “vehicles” as used herein refer to carrier materials suitable for incorporation in a topically applied composition. Carriers and vehicles useful herein include any such materials known in the art, which are non-toxic and do not interact with other components of the formulation in which it is contained in a deleterious manner.
  • aqueous refers to a formulation that contains water or that becomes water-containing following application to the skin or mucosal tissue.
  • Cream bases are water-washable, and contain an oil phase, an emulsifier, and an aqueous phase.
  • the oil phase also called the "internal” phase, is generally comprised of petrolatum and a fatty alcohol such ascetyl or stearyl alcohol.
  • the aqueous phase usually, although not necessarily, exceeds the oil phase in volume, and generally contains a humectant.
  • the emulsifier in a cream formulation is generally a nonionic, anionic, cationic or amphoteric surfactant.
  • Lotions are preparations to be applied to the skin surface without friction, and are typically liquid or semiliquid preparations in which particles, including the active agent, are present in a water or alcohol base. Lotions are usually suspensions of solids, and preferably, comprise a liquid oily emulsion of the oil-in-water type. Lotions are preferred formulations herein for treating large body areas, because of the ease of applying a more fluid
  • Lotions will typically contain suspending agents to produce better dispersions as well as compounds useful for localizing and holding the active agent in contact with the skin, e.g., methylcellulose, sodium carboxymethyl-cellulose, or the like.
  • Solutions are homogeneous mixtures prepared by dissolving one or more chemical substances (solutes) in a liquid such that the molecules of the dissolved substance are dispersed among those of the solvent.
  • the solution can contain other pharmaceutically or cosmetically acceptable chemicals to buffer, stabilize or preserve the solute.
  • solvents used in preparing solutions are ethanol, water, propylene glycol or any other acceptable vehicles.
  • gels are semisolid, suspension-type systems.
  • Single-phase gels contain organic macromolecules distributed substantially uniformly throughout the carrier liquid, which is typically aqueous, but also, preferably, contain an alcohol, and, optionally, an oil.
  • organic macromolecules i.e., gelling agents, are cross-linked acrylic acid polymers such as the "carbomer” family of polymers, e.g., carboxypolyalkylenes that can be obtained commercially under the Carbopol trademark.
  • hydrophilic polymers such as polyethylene oxides, polyoxyethylene-polyoxypropylene copolymers and polyvinylalcohol
  • cellulosic polymers such as hydroxy-propyl cellulose, hydroxyethyl cellulose, hydroxypropyl methylcellulose, hydroxy-propyl methylcellulose phthaiate, and methylcellulose
  • gums such as tragacanth and xanthan gum
  • sodium alginate and gelatin
  • dispersing agents such as alcohol or glycerin can be added, or the gelling agent can be dispersed by trituration, mechanical mixing or stirring, or combinations thereof.
  • Ointments are semisolid preparations that are typically based on petrolatum or other petroleum derivatives.
  • the specific ointment base to be used is one that will provide for a number of desirable characteristics, e.g., emolliency or the like.
  • an ointment base should be inert, stable, nonirritating, and nonsensitizing.
  • ointment bases can be grouped in four classes: oleaginous bases;
  • Oleaginous ointment bases include, for example, vegetable oils, fats obtained from animals, and semisolid hydrocarbons obtained from petroleum.
  • Emulsifiable ointment bases also known as absorbent ointment bases, contain little or no water and include, for example, hydroxystearin sulfate, anhydrous lanolin, and hydrophilic petrolatum.
  • Emulsion ointment bases are either water-in-oil (W/O) emulsions or oil- in- water (O/W) emulsions, and include, for example, acetyl alcohol, glyceryl monostearate, lanolin, and stearic acid.
  • W/O water-in-oil
  • O/W oil- in- water
  • Preferred water-soluble ointment bases are prepared from polyethylene glycols of varying molecular weight; see Remington: The Science and Practice of Pharmacy for further information.
  • Pastes are semisolid dosage forms in which the active agent is suspended in a suitable base. Depending on the nature of the base, pastes are divided between fatty pastes or those made from single-phase aqueous gels.
  • the base in a fatty paste is generally petrolatum or hydrophilic petrolatum or the like.
  • the pastes made from single-phase aqueous gels generally incorporate carboxymethylcellulose or the like as a base.
  • Enhancers are lipophilic co-enhancers typically referred to as "plasticizing" enhancers, i.e., enhancers that have a molecular weight in the range of about 150 to 1000, an aqueous solubility of less than about 1 wt.%, preferably less than about 0.5 wt.%, and most preferably less than about 0.2 wt.%.
  • the Hildebrand solubility parameter ⁇ of plasticizing enhancers is in the range of about 2.5 to about 10, preferably in the range of about 5 to about 10.
  • Preferred lipophilic enhancers are fatty esters, fatty alcohols, and fatty ethers.
  • fatty acid esters examples include methyl laurate, ethyl oleate, propylene glycol nionolaurace, propylene glycerol dilaurate, glycerol mono laurate, glycerol
  • Fatty alcohols include, for example, stearyl alcohol and oleyl alcohol, while fatty ethers include compounds wherein a diol or triol, preferably a C2-C4 alkane diol or triol, are substituted with one or two fatty ether substituents. Additional permeation enhancers will be known to those of ordinary skill in the art of topical drag delivery, and/or are described in the pertinent texts and literature. See, e.g., Percutaneous Penetration Enhancers, eds. Smith et al. (CRC Press, 1995)(incorporated herein by reference herein in its entirety).
  • compositions of the present invention can be included in addition to those identified above.
  • additives include, but are not limited to, antioxidants, astringents, perfumes, preservatives, emollients, pigments, dyes, humectants, propellants, and sunscreen agents, as well as other classes of materials whose presence can be
  • Typical examples of optional additives for inclusion in the formulations of the present invention are as follows: preservatives such as sorbate; solvents such as isopropanol and propylene glycol; astringents such as menthol and ethanol; emollients such as polyalkylene methyl glucosides; humectants such as glycerine; emulsifiers such as glycerol stearate, PEG- 100 stearate, polyglyceryl-3 hydroxylaury 1 ether, and polysorbate 60; sorbitol and other polyhydroxyalcohols such as polyethylene glycol;
  • preservatives such as sorbate
  • solvents such as isopropanol and propylene glycol
  • astringents such as menthol and ethanol
  • emollients such as polyalkylene methyl glucosides
  • humectants such as glycerine
  • emulsifiers such as
  • sunscreen agents such as octyl methoxyl cinnamate (available commercially as Parsol MCX) and butyl methoxy benzoylmethane (available under the tradename Parsol 1789); antioxidants such as ascorbic acid (vitamin C), a- tocopherol (Vitamin E), ⁇ -tocopherol, ⁇ - tocopherol, ⁇ -tocopherol, ⁇ -tocopherol, ⁇ -tocopherol, ⁇ ⁇ - tocopherol, ⁇ -tocopherol, and retinol (vitamin A); essential oils, ceramides, essential fatty acids, mineral oils, vegetable oils (e.g., soya bean oil, palm oil, liquid fraction of shea butter, sunflower oil), animal oils (e.g., perhydrosqualene), synthetic oils, silicone oils or waxes (e.g., cyclomethicone and dimethicone), fluorinated oils (generally perfluoropol
  • conditioners and moisturizing agents include, by way of example, pyrrolidine carboxylic acid and amino acids; organic antimicrobial agents such as 2,4,4'- trichloro-2 -hydroxy diphenyl ether (triclosan) and benzoic acid; anti- inflammatory agents such as acetylsalicylic acid and glycyrrhetinic acid; anti-seborrhoeic agents such as retinoic acid; vasodilators such as nicotinic acid; inhibitors of melanogenesis such as kojic acid; and mixtures thereof.
  • beneficial agents such as those materials that condition the skin (particularly, the upper layers of the skin in the stratum corneum) and keep it soft by retarding the decrease of its water content and/or protect the skin.
  • Such conditioners and moisturizing agents include, by way of example, pyrrolidine carboxylic acid and amino acids; organic antimicrobial agents such as 2,4,4'- trichloro-2 -hydroxy diphenyl
  • Further additional active agents including, for example, alpha hydroxyacids, alpha ketoacids, polymeric hydroxyacids, moisturizers, collagen, marine extract, and antioxidants such as ascorbic acid (Vitamin C), a-tocopherol (Vitamin E), ⁇ - tocopherol, ⁇ -tocopherol, 6- tocopherol, ⁇ -tocopherol, ⁇ -tocopherol, ⁇ 2 - tocopherol, ⁇ - tocopherol, and retinol (Vitamin A), and/or pharmaceutically acceptable salts, esters, amides, or other derivatives thereof.
  • a preferred tocopherol compound is a-tocopherol.
  • Additional agents include those that are capable of improving oxygen supply in skin tissue, as described, for example, in Gross, et al, WO 94/00098 and Gross, et ah, WO 94/00109, both assigned to Lancaster Group AG (incorporated herein by reference in their entirety). Sunscreens and UV absorbing compounds can also be included.
  • Non-limiting examples of such sunscreens and UV absorbing compounds include aminobenzoic acid (PABA), avobenzone, cinoxate, dioxybenzone, homosalate, menthyl anthranilate, oxtocrylene, octyl methoxycmnamate, octyl salicylate, oxybenzone, padirnate O, phenylbenzirmdazole sulfonic acid, sulisobenzone, titanium dioxide, trolamine salicylate, zinc oxide, ensulizole, meradiraate, octinoxate, octisalate, and octocrylene. See Title 21. Chapter 1. Subchapter D. Part 352.
  • “Sunscreen drug products for over-the-counter human use” incorporated herein in its entirety.
  • Other embodiments can include a variety of non-carcinogenic, non-irritating healing materials that facilitate treatment with the formulations of the invention.
  • healing materials can include nutrients, minerals, vitamins, electrolytes, enzymes, herbs, plant extracts, glandular or animal extracts, or safe therapeutic agents that can be added to the formulation to facilitate the healing of dermal disorders.
  • the present invention contemplates amounts of these various additives equivalent to those conventionally used in the cosmetics field, and range, for example, from about 0.01 % to about 20% of the total weight of the topical formulation.
  • the formulations of the invention can also include conventional additives such as opacifiers, fragrance, colorant, stabilizers, surfactants, and the like.
  • other agents can also be added, such as antimicrobial agents, to prevent spoilage upon storage, i.e., to inhibit growth of microbes such as yeasts and molds.
  • Suitable antimicrobial agents for the present invention include, but are not limited to the following selected from the group consisting of the methyl and propyl esters of p- hydroxybenzoic acid (i.e., methyl and propyl paraben), sodium benzoate, sorbic acid, imidurea, and combinations thereof.
  • other agents can also be added, such as repressors and inducers, i.e., to inhibit (i.e., glycose) or induce (i.e. xylose) the production of the polypeptide of interest.
  • Such additives can be employed provided they are compatible with and do not interfere with the function of the formulations.
  • the formulations can also contain irritation-mitigating additives to minimize or eliminate the possibility of skin irritation or skin damage resulting from the chemical entity to be administered, or other components of the composition.
  • Suitable irritation-mitigating additives include, for example: a-tocopherol
  • monoamine oxidase inhibitors particularly phenyl alcohols such as 2-phenyl- 1 -ethanol; glycerin; salicylates; ascorbates; ionophores such as monensin; amphophilic amines;
  • the irritation-mitigating additive if present, can be incorporated into the compositions at a concentration effective to mitigate irritation or skin damage, typically representing not more than about 20 wt.%, more typically not more than about 5 wt.%, of the formulation.
  • pharmacologically active agents that can be incorporated into the present formulations in certain embodiments and thus topically applied along with the active agent include, but are not limited to, the following: agents that improve or eradicate pigmented or non-pigmented age spots, keratoses, and wrinkles; antimicrobial agents; antibacterial agents; antipruritic and antixerotic agents; ant i- inflammatory agents; local anesthetics and analgesics; corticosteroids; retinoids;
  • topical pharmacologically active agents include acyclovir, amphotericins, chlorhexidine, clotrimazole, ketoconazole, econazole, miconazole, metronidazole, minocycline, nystatin, neomycin, kanamycin, phenytoin, para-amino benzoic acid esters, octyl methoxycmnamate, octyl salicylate, oxybenzone, dioxybenzone, tocopherol, tocopheryl acetate, selenium sulfide, zinc pyrithione, diphenhydramine, pramoxine, lidocaine, procaine, erythromycin, tetracycline, clindamycin, crotamiton, hydroquinone and its monomethyl and benzyl ethers, naproxen, ibuprofen, cromolyn, retin
  • a cream, lotion, gel, ointment, paste or the like can be spread on the affected surface and gently rubbed in.
  • a solution can be applied in the same way, but more typically will be applied with a dropper, swab, or the like, and carefully applied to the affected areas.
  • the application regimen will depend on a number of factors that can readily be determined, such as the severity of the condition and its responsiveness to initial treatment, but will normally not involve more than one application per day.
  • One of ordinary skill can readily determine the optimum amount of the formulation to be administered, administration methodologies and repetition rates. In general, it is contemplated that the formulations of the invention will be applied in the range of once or twice weekly up to once daily.
  • the invention provides methods for treating a skin disease, wherein the methods comprise administering to a subject in need of such treatment a genetically engineered microorganism, e.g., genetically engineered bacteria, capable of expressing a recombinant therapeutic fusion protein of the invention, thereby treating the subject.
  • a genetically engineered microorganism e.g., genetically engineered bacteria
  • the disease is atopic dermatitis.
  • the recombinant therapeutic fusion protein comprises filaggrin.
  • the recombinant therapeutic fusion protein comprises filaggrin operably linked to a cell penetrating peptide.
  • the recombinant therapeutic fusion protein is operably linked to an export signal. Kits
  • kits comprising (a) a composition of the invention and (b) instructions for use thereof.
  • a kit of the invention comprises (a) any one of the live biotherapeutic compositions of the invention, and (b) instructions for use thereof. Instructions can include an explanation of how to apply, administer, use, and maintain the compositions.
  • the compositions of the invention are described supra.
  • a composition of the invention is an engineered microorganism capable of expressing therapeutically relevant recombinant fusion polypeptides, as described supra.
  • the composition comprises engineered bacteria (e.g., S. epidermidis) capable of expressing a recombinant fusion polypeptide comprising filaggrin.
  • a kit can include a sealed container.
  • containers include a bottle, a metal tube, a laminate tube, a plastic tube, a dispenser, a pressurized container, a barrier container, a package, a compartment, a lipstick container, a compact container, cosmetic pans that can hold cosmetic compositions, or other types of containers such as injection or blow-molded plastic containers into which the dispersions or compositions or desired bottles, dispensers, or packages are retained.
  • Other examples of containers include glass or plastic vials or bottles.
  • the kit and/or container can include indicia on its surface. The indicia, for example, can be a word, a phrase, an abbreviation, a picture, or a symbol.
  • EXAMPLE 1 Development of a nucleic acid construct that can encode a protein capable of being exported out of the 5. epidermidis cell and then imported into human keratinocytes
  • the invention describes in one embodiment the generation of a recombinant S.
  • S. epidermidis strains that is capable of heterologous protein secretion, therefore overcoming the intractability of genetic modification of S. epidermidis.
  • Functional genetic analyses of the common skin colonizers S. aureus and S. epidermidis have previously been limited due to the presence of Type I and IV restriction systems in virtually all strains of these bacteria. These restriction systems recognize methylated cytosine bases in DNA from standard clone expansion systems such as DH10B E. coli.
  • DCIOB a methylation deficient E. coli strain, DCIOB, several constructs have been created in S. epidermidis strain ATCC12228 5 , which is a commensal, non-pathogenic isolate lacking ica operons implicated in S.
  • the invention describes the first known reported heterologous protein expression in S. epidermidis.
  • the present invention thus provides, in one embodiment, a nucleic acid plasmid capable of encoding a protein that is exported out of the S. epidermidis cell and subsequently imported into human keratinocytes.
  • This plasmid, pAZT is based on pJB38 (Bose, J. L., et al. Applied and environmental microbiology. 2013;79(7):2218-2224), an allelic exchange E. coli- staphylococcal shuttle vector, which has been specifically re-engineered to possess features that improve functionality.
  • the present invention provides, in one embodiment, an engineered S. epidermidis capable of effectively colonizing reconstituted epidermis and that is capable of producing 50 ⁇ g of protein per mL of ⁇ 10 9 CFU/mL (FIG. 2).
  • CPP Cell penetrating peptides
  • the present invention in one embodiment, provides a construct that utilizes such an approach, and comprises an HIV trans-activator of a transcription-derived cell-penetration peptide (RMR) protein motif (FIG. 2).
  • RMR transcription-derived cell-penetration peptide
  • FOG. 2 transcription-derived cell-penetration peptide
  • the present invention uses an auxotrophic strain, which requires supplementation of key amino acids (D-ala) or a certain metabolic gene (AlaR) for survival, and simultaneously replaces the need for an antibiotic resistant strain for selection, the latter of which is not commercially viable.
  • the present invention integrates a "kill switch", which is based on
  • the present invention provides cell counters, which recombine out the AZT locus after a defined number of divisions, although this method would necessitate reapplication of the vehicle.
  • a CRISPR/Cas9-based kill switch which is xylose-inducible and doubly regulated with a theophylline riboswitch, was developed.
  • Cas9 is extremely efficient at chromosomal cleavage given a targeting guide, and since staphylococci lack canonical non-homologous end joining repair pathways, genomic cleavage results in death in the absence of a homologous recombination template.
  • the use of a CRISPR-based system also confers great specificity, since comparative genomics can be used to design guides unique to the engineered S. epidermidis strain of the present invention, such that the construct is inactive if spread to other microbes by horizontal gene transfer.
  • the present invention provides a construct designed to express multiple CRISPR spacers to simultaneously target multiple genomic regions to ensure cleavage and minimize survival by reversion.
  • EXAMPLE 2 Determine the persistence and localization of topically applied S.
  • SE-sGFP sGFP-expressing strain of S. epidermidis
  • the RHE was intentionally punctured with a Derma Microneedle device to determine localization of the bacteria in the presence of damaged skin.
  • Non-fluorescence based detection of therapeutic proteins The therapeutic proteins ultimately delivered are not be fluorescent, and further, suitable antibodies to characterize their delivery to epidermis may not be available.
  • Proteomic analysis of tape strips of the stratum corneum has been used to characterize differences in in vivo protein profiles from patients with atopic dermatitis (Sakabe, J., et al. The Journal of allergy and clinical immunology. 2014;134(4):957-960 e958) and ichthyosis (Rice, R.H., et al. PloS one.
  • EXAMPLE 4 Evaluate pharmacokinetics (PK) and pharmacodynamics (PD) of AZT- 01 in mice (non-GLP)
  • a genetic atopic dermatitis mouse construct (flaky tail mice) was used to assess the PK/PD of AZT-01, while the PK of AZT-01 was assessed in healthy mice.
  • AZT-01 was topically applied to mice and the PD was assessed via phenotypic (erythema, edema, excoriation, dryness, and transepidermal water loss) and histological changes (skin barrier recapitulation, fibrosis, CD4+ T cells, etc.).
  • phenotypic erythema, edema, excoriation, dryness, and transepidermal water loss
  • histological changes skin barrier recapitulation, fibrosis, CD4+ T cells, etc.
  • Atopic dermatitis mouse models In order to investigate the applicability of the approach, two model mouse systems were used: the filaggrin knockout mouse (flg-l-) and the flaky tail mouse (ft/ft).
  • flg-l- filaggrin knockout mouse
  • ft/ft flaky tail mouse
  • flg-l- mice exhibit dry, scaly skin. Despite marked decreases in natural moisturizing factor levels, which are filaggrin degradation products, stratum corneum (SC) hydration and transepidermal water loss (TEWL) were normal in flg-l- mice. Antigens penetrated the flg-l- SC more efficiently, leading to enhanced responses in hapten- induced contact
  • Fig Filaggrin
  • mice were randomized into the following treatment groups: topical vehicle control (50% glycerol, 50% sterilized BHI medium), topical recombinant filaggrin (purified recombinant filaggrin in 50 ⁇ glm ), topical wild type Staphylococcus Epidermidis (SE) (l.OxlO 9 CFU in 50% glycerol), and topical SE FLG (l.OxlO 9 CFU in 50% glycerol).
  • SE Staphylococcus Epidermidis
  • SE topical SE FLG
  • Each solution was applied to the same ear on each mouse on days 0, 7, 14, and 21, and mice were also assessed on these days before application of the appropriate solution. Final assessment occurred on day 28 after which point the mice was sacrificed according to the appropriate animal protocols.
  • the primary outcome (described in detail below) is the change in clinical disease score, which assessed macroscopic changes in disease presentation.
  • mice per arm per genotype was required in order to detect a mean change of 4 points in the clinical disease score between groups. This means that a total of 32 mice per genotype (for a total of 64 mice) were needed for the study.
  • Clinical disease score In order to measure the effect of treatment on the macroscopic and microscopic changes associated with treatment of SE , a clinical score based on previous studies was used (see, e.g., Matsuoka H., et al. Allergy.
  • the composite clinical disease score is the sum of the degree of severity of erythema, edema, excoriation and dryness on the ear surface was scored as 0 (not visible), 1 (mild), 2 (moderate) and 3 (severe), accordingly. Scoring was performed by individual who was blinded to treatment status of each group. Skin was photographed every 7 days.
  • Dysbiosis was measured using ecological metrics and community structure analyses. First, dysbiosis was assessed as a function of diversity using the Shannon Diversity Index, which is an ecological measure of microbial communities that considers and was compared before and after application. Additionally, community structures of the local microbiome was compared before and after treatment. Dysbiosis was then measured as % overall deviation from (i) the baseline microbiome, and (ii) deviation from the mean community structure across our controls using statistics such as the Yue-Clayton index that compares community structures. Finally, microbiome trends was analyzed on a per-species level. The longitudinal dynamics of each species was also tracked over the treatments, to identify whether species are being lost from the community.
  • Filaggrin was visualized and quantified using immunocytochemistry by comparing AZT-01 to a vehicle control. Keratinocytes cells were fixed with 70% ethanol, 50 mM glycine for 1 hour. Immunofluorescence staining was performed by incubation of ant i- filaggrin primary antibody at 1:200 for 2 hours, followed by incubation with rat anti-goat rhodamine secondary antibody (Jackson Laboratory) at 1:200 dilutions in the presence of Hoechst Stain Solution (Sigma). Slides were mounted with coverslips in Gel/Mount (Biomed).
  • Immunofluorescence Microscopy was used to visualize filaggrin localization. Mouse skin samples were fixed in 10% formalin and paraffin embedded. Paraffin sections were dewaxed and washed with 95% ethanol followed by methanol hydrogen peroxide. The sections were then treated with a heat induced epitope retrieval (HIER) procedure using rodent Decloaker solution (Biocare Medical, RD913) and the Biocare decloaking chamber. After being washed in Tris pH 7.4, sections were incubated in the presence of rat serum and FcBlock (24G2) followed by rabbit anti-Escherichia coli B (DAKO, B0357) diluted in the blocking solution.
  • HIER heat induced epitope retrieval
  • EXAMPLE 5 AZT-01 and its effects on local and systemic inflammation and immunity in rats (non-GLP).
  • tissue samples were analyzed for histologic changes in inflammatory activity ⁇ e.g., quantification CD4+ T cells, Langerhans cells, IgE, IL-4, IFN- ⁇ , etc.) as well as activity and changes in the cutaneous immune response ⁇ e.g., quantitation of IL-4, IL-10, IL-13, etc.).
  • Clinical signs of potential side effects related to the use of therapy including erythema, skin temperature changes, edema, blistering, and ulcerations were also monitored.
  • RNA transcript quantification Variable expression of genes associated with atopic dermatitis development, progression, and maintenance (AD-associated pathogenic cytokines ⁇ e.g., IL-4, IL-5, IL-13, INF- ⁇ , IL-17, IL-10 and TNF-a)) were measured by standard qPCR assays. Briefly, total RNA from the skin samples were isolated using the Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer's instructions. The respective cDNA were synthesized using reverse transcriptase PCR (RT- PCR). Real-time PCR was performed using the comparative 2-AACT method and was normalized to Glyceraldehyde 3 -phosphate dehydrogenase (GAPDH) transcript levels.
  • GPDH Glyceraldehyde 3 -phosphate dehydrogenase
  • AZT- 01 As a measure of safety, signs of AZT- 01 becoming blood-borne was monitored by taking samples of skin-draining lymph nodes (DLNs) and the spleen of one mouse after two weeks of application of AZT-01. Briefly, the mouse was placed in 70% EtOH and moved to a laminar flow hood. After 1-2 minutes in EtOH, DLNs and spleen was isolated in a 50-mL conical tube with a 70 ⁇ m strainer and was processed as separate samples. The organs were dissociated with 500 ⁇ of sterile PBS, and 50-100 ⁇ of cell suspension was cultured on BHI agar media.
  • DLNs skin-draining lymph nodes
  • EXAMPLE 6 Conduct initial formulation and analytical method development to evaluate a proposed set of specifications for the active pharmaceutical ingredient (API) and the drug product (DP).
  • API active pharmaceutical ingredient
  • DP drug product
  • LBP live biotherapeutic product
  • API active pharmaceutical ingredient
  • DP drug product
  • Human filaggrin (hFLG) is comprised of 12 repeating units and is processed by intracellular proteases to release the individual units. The sequences within these units are highly homologous. It has been proposed that the units are cleaved at "linker regions.” The segments between these linker regions are the individual units, with each unit containing a pair of sub-domains.
  • the entire human filaggrin (hFLG) sequence (Uniprot P20930) was analyzed using the on-line Kite-Doolittle calculation tool (https://web.expasy.org/protscale/).
  • the hydrophobicity score as a function of amino acid position graph is shown in FIG. 7. As shown in FIG. 7, there is a periodic increase in hydrophobicity.
  • Kite-Doolittle score gave the highest differential between the highest and lowest values.
  • mFLG sequence NCBI Reference Sequence: XP_017175331.1
  • the molecular regions of interest were examined further. It was found that the distance between the crests which correspond to the more hydrophobic regions was farther in the human filaggrin than in the mouse. Also, the maximum hydrophobicity was found to be higher in the mouse than in human.
  • FIG. 9 shows the region of hFLG starting at amino acid 1400 to 1800, with the unit segment of domains 9 and 10 shown. The repeat end at a peak that comes right after the 10 amino acid segment that is common to human and mouse filaggrin (SGSQASDSEGHS) is also shown. The high peaks at positions 1444 and 1767 of the graph correspond to the FLY segments. The peaks at 1679 and 1929 are regions containing poly-tyrosines.
  • the protein hFLG Domains 9-10) (1429-1774) (SEQ ID NO: 2) represents the high- to-high hydrophobicity segments. The segment is shown in FIG. 10. It contains the FLY segments at both ends of the protein. SEQ ID NO: 2
  • repeating the FLY segments may not be required for activity, and further, it may be a burden for bacteria and may be the source of the lack of production in a Gram positive organism.
  • FIG. 10 is a graph that shows hydrophobicity score as a function of amino acid position for hFLG[9-10](1429-1774) from amino acid position 1400 to amino acid position 1800 in hFLG.
  • hFLG [domain 9-10] proteins with systematically shaved off regions of the N- terminus were produced.
  • the graph in FIG. 11 shows that the start and end positions of the hFLG [9-10] 1429- 1777) (SEQ ID NO: 2) may be too long. Therefore, the N-terminal FLY segment was cut to make hFLG [9-10] (1452-1777) (SEQ ID NO: 4) to prevent unwanted recombination events.
  • Theoretical pl/Mw 10.65 / 36162.11 Selection of segment based on “A " shape ("low-high-low” )
  • SEQ ID NO: 5 a protein based on the low-to-low segment hFLG[9-10](1545-1869) was made, shown below as SEQ ID NO: 5.
  • Theoretical pl/Mw 10.07 / 26329.02 It is further contemplated that on hFLG[9-10](1452-1777) (SEQ ID NO: 2), the N- terminus region would be knocked off.
  • the hFLG[9-10] sequence (SEQ ID NO: 1) was subjected to a BLAST analysis:
  • hFLG[M-AZT-mutein-RMR](l-352) was created, shown below as SEQ ID NO: 8.
  • a human filaggrin consensus sequence was generated by alignment of filaggrin dimers hFLG[3-4], hFLG[5-6], hFLG[7-8], hFLG[9-10], hFLG[l l-12], hFLG[13-14], hFLG[15-16], hFLG[17-18], hFLG[19-20], hFLG[21-22] as shown in FIG. 13.
  • the consensus sequence shown as SEQ ID NO: 9 refers to the sequence formed from the most frequently occurring amino acids shown in the alignment in FIG. 13.
  • Keratin Extraction from human callus was used to measure activity of various hFLG[9-10] sequences set forth in SEQ ID NOs 1-9. Keratin Extraction from human callus:
  • Keratins were extracted from human callus. One to two grams of callus was homogenized in 10 mL 5mM Tris pH 7.4 with protease inhibitors using a BULLET
  • BLENDER bead beater Homogenized tissue was centrifuged 10 000 rpm for 20 minutes at 4°C. The resulting pellet was resuspended in 0.05M tris pH 7.4 containing 8 M urea and 0.025mM ⁇ -mercaptoethanol and mixed gently for 2h at 37°C. The urea lysate was centrifuged 10 000 rpm for 10 minutes. The supernatant was dialyzed against 5mM Tris pH7.4 overnight at 4°C allowing the gradual assembly of keratin filaments.
  • Plates were washed 3 times with 200 ⁇ ⁇ per well of PBST.
  • an ant i- filaggrin IgY chicken antibody (RL-012-001B antibody 1/1000 in PBST) was added to the wells.
  • 200 ⁇ ⁇ of a mouse pan-keratin antibody (Type II AE3 Ab at a dilution of 1/500 in PBST) was added to indicated wells.
  • Primary antibodies were incubated at room temperature with shaking for lh. Primary antibodies were removed and plates washed 3 times with PBST.
  • HRP horse radish peroxidase
  • FIGS. 14-16 demonstrate that there was differential binding to keratin among the hFLG sequences tested.
  • FIG. 14 is a graph that shows background FLG binding at ⁇ g/well for 2h at 37°C.
  • the results shown in FIG. 14 include non specific binding (NSB).
  • FIG. 15 is a graph that shows the binding of various hFLG segments to human callus keratin (with NSB removed).
  • FIG. 16 is a graph that shows titration of IgY anti-hFLG. As shown in FIGS. 14-16, hFLG[5-6] did not bind keratin, while the various hFLG[9-10] sequences that were tested showed binding to keratin.
  • EXAMPLE 12 Activity of hFLG[9- 10] -Secreting SE in Mice.
  • Fig-/- mice A genetic IV mouse model (Fig-/-) will be used, as well as wild type mice to assess colonization dynamics of FLG-producing SE in vivo.
  • Fig-/- mice are filaggrin deficient and exhibit dry, scaly skin. Despite marked decreases in natural moisturizing factor levels, which are filaggrin degradation products, stratum corneum (SC) hydration and TEWL are normal in Fig- 1- mice.
  • Fig-/- mice are obtained from RIKEN BioResource Research Center (RIKEN BRC, Tsukuba, Ibaraki, Japan). Wild type mice (BALB/c) will also be used in this experiment.
  • the hFLG[9-10] sequences set forth in SEQ ID NOs 1-9 will be used in SE to Flg-/- and BALB/c mice. The study will be conducted for four weeks using five groups in each mouse type. Mice will be assigned into the following treatment groups: topical vehicle control (50% glycerol, 50% sterilized BHI medium), topical wild type SE (1.0x10 s CFU/cm 2 in 50% glycerol), and three doses of each of each filaggrin- secreting SE constructs (SE FLG )
  • mice (10 6 , 107 , and 108 CFU/cm 2 in 50% glycerol). Each solution will be applied to the same ear and tail on each mouse daily for seven days, and mice be assessed on days 7, 14, 30, and 60 for microbiome analyses to assess colonization dynamics and on days 7 and 14 for microscopy and histology to assess localization and macroscopic changes in the skin (e.g., any signs of adverse events such as inflammation), etc. 12 mice in each arm per mouse type will be used.

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Abstract

La présente invention concerne des plasmides isolés, des micro-organismes de recombinaison, des kits et des procédés pour le traitement d'une maladie cutanée inflammatoire.
PCT/US2018/049477 2017-09-05 2018-09-05 Procédés et compositions pour traiter une maladie cutanée inflammatoire WO2019050898A1 (fr)

Priority Applications (7)

Application Number Priority Date Filing Date Title
EP18854435.7A EP3678640A4 (fr) 2017-09-05 2018-09-05 Procédés et compositions pour traiter une maladie cutanée inflammatoire
AU2018328119A AU2018328119A1 (en) 2017-09-05 2018-09-05 Methods and compositions for treating inflammatory skin disease with recombinant microorganisms
CA3074823A CA3074823A1 (fr) 2017-09-05 2018-09-05 Procedes et compositions pour traiter une maladie cutanee inflammatoire
KR1020207009609A KR20200051001A (ko) 2017-09-05 2018-09-05 재조합 미생물을 사용하여 염증성 피부 질환을 치료하기 위한 방법 및 조성물
CN201880071303.9A CN111278447A (zh) 2017-09-05 2018-09-05 用重组微生物治疗炎性皮肤疾病的方法和组合物
JP2020513607A JP2020536499A (ja) 2017-09-05 2018-09-05 組換え微生物を用いて炎症性皮膚疾患を処置するための方法および組成物
JP2023160723A JP2024009822A (ja) 2017-09-05 2023-09-25 組換え微生物を用いて炎症性皮膚疾患を処置するための方法および組成物

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US11850267B2 (en) 2018-04-05 2023-12-26 Azitra Inc Methods and compositions for treating skin disease with recombinant microorganisms
WO2020206221A1 (fr) * 2019-04-05 2020-10-08 Azitra Inc Procédés et compositions pour traiter une dermatite atopique avec des microorganismes recombinants
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JP2024009822A (ja) 2024-01-23
KR20200051001A (ko) 2020-05-12
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CA3074823A1 (fr) 2019-03-14
AU2018328119A1 (en) 2020-04-02

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